BN0348 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 6.1144e-08 5.2158e-06
Layer 3 5.7825e-07 3.4096e-04
Layer 5 9.1791e-07 8.6081e-05
Layer 2 3.8620e-06 5.3672e-03
Layer 6 2.6970e-05 2.6687e-03
Layer 1 9.6830e-01 6.7635e-01
WM 9.9811e-01 9.0088e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
INPP5F Expression Distribution
Gene Specificity Score (GSS)
INPP5F GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
INPP5F Layer 4 2.5449 0.7261
FBXW7 Layer 4 2.5176 0.7242
SLC9A6 Layer 4 2.5273 0.7214
SH3GL2 Layer 6 2.3623 0.7174
CNTNAP1 Layer 4 2.5117 0.7137
KIFAP3 Layer 4 2.5537 0.7120
ELAVL4 Layer 4 2.6953 0.7111
CABP1 Layer 4 2.3525 0.7096
NAP1L5 Layer 4 2.6191 0.7090
NCOA7 Layer 4 2.5928 0.7078
SNCA Layer 5 2.2773 0.7053
CCDC92 Layer 4 2.3281 0.7051
CHGA Layer 4 2.3838 0.7047
CAB39 Layer 5 2.3086 0.7045
GUCY1B1 Layer 4 2.3340 0.7033
CAP2 Layer 4 2.4785 0.7020
TUBB3 Layer 4 2.3242 0.7013
PRUNE2 Layer 5 2.7012 0.7006
TSPAN13 Layer 4 2.5332 0.7006
INA Layer 4 2.5332 0.7004
NUDT4 Layer 5 2.6426 0.7001
LDHA Layer 5 2.3184 0.6990
G3BP2 Layer 4 2.3525 0.6986
GOT1 Layer 5 2.3281 0.6984
EFR3A Layer 4 2.7969 0.6982
DNAJC6 Layer 5 2.2578 0.6978
UBE2L3 Layer 4 2.5059 0.6976
CAMK2D Layer 5 2.9336 0.6975
HK1 Layer 4 2.3184 0.6972
VPS35 Layer 4 2.3525 0.6971
PFKP Layer 4 2.5176 0.6970
CPLX1 Layer 4 2.5000 0.6969
SCOC Layer 4 2.4395 0.6967
HERC1 Layer 4 2.5176 0.6962
MAPK10 Layer 4 2.3896 0.6957
SPRYD3 Layer 4 2.3926 0.6957
NRN1 Layer 4 2.4121 0.6954
CEND1 Layer 4 2.2949 0.6954
STRAP Layer 4 2.4697 0.6951
GLS Layer 4 2.4297 0.6950
NAP1L2 Layer 4 2.3340 0.6946
CDK14 Layer 4 2.7363 0.6946
RUFY3 Layer 4 2.2344 0.6934
SNAP91 Layer 4 2.5840 0.6934
TUBB4B Layer 4 2.3242 0.6924
TRIM37 Layer 5 2.5215 0.6921
MAP6 Layer 4 2.4082 0.6920
GABRG2 Layer 4 2.6133 0.6918
ATXN7L3B Layer 4 2.4570 0.6917
AAK1 Layer 4 2.5605 0.6912

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN0348
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN0348_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0348/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0348/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0348/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0348/report/PD/BN0348_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0348/report/PD/BN0348_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-10 23:55:19
  • Number of Processes: 10
  • Spending Time: 0h 3m